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Van Dinh Q, Liu J, Dutta P. Effect of Slp4-a on Membrane Bending During Prefusion of Vesicles in Blood-Brain Barrier. J Biomech Eng 2023; 145:011006. [PMID: 35838328 PMCID: PMC9445323 DOI: 10.1115/1.4054985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 07/08/2022] [Indexed: 11/08/2022]
Abstract
Vesicle exocytosis is a promising pathway for brain drug delivery through the blood-brain barrier to treat neurodegenerative diseases. In vesicle exocytosis, the membrane fusion process is initiated by the calcium sensor protein named synaptotagmin-like protein4-a (Slp4-a). Understanding conformational changes of Slp4-a during the prefusion stage of exocytosis will help to develop vesicle-based drug delivery to the brain. In this work, we use molecular dynamics (MD) simulations with a hybrid force field coupling united-atom protein model with MARTINI coarse-grained (CG) solvent to capture the conformational changes of Slp4-a during the prefusion stage. These hybrid coarse-grained simulations are more efficient than all-atom MD simulations and can capture protein interactions and conformational changes. Our simulation results show that the calcium ions play critical roles during the prefusion stage. Only one calcium ion can remain in each calcium-binding pocket of Slp4-a C2 domains. The C2B domain of calcium-unbound Slp4-a remains parallel to the endothelial membrane, while the C2B domain of calcium-bound Slp4-a rotates perpendicular to the endothelial membrane to approach the vesicular membrane. For the calcium-bound case, three Slp4-a proteins can effectively bend lipid membranes at the prefusion stage, which could later trigger lipid stalk between membranes. This work provides a better understanding how C2 domains of Slp4-a operate during vesicle exocytosis from an endothelial cell.
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Affiliation(s)
- Quyen Van Dinh
- School of Mechanical and Materials Engineering, Washington State University, Pullman, WA 99164-2920
| | - Jin Liu
- School of Mechanical and Materials Engineering, Washington State University, Pullman, WA 99164-2920
| | - Prashanta Dutta
- School of Mechanical and Materials Engineering, Washington State University, Pullman, WA 99164-2920
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2
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Awasthi A, Kumar N, Mishra A, Ravi R, Dalal A, Shankar S, Chandra R. Noscapine-Amino Acid Conjugates Suppress the Progression of Cancer Cells. ACS Pharmacol Transl Sci 2022; 5:1292-1304. [PMID: 36524011 PMCID: PMC9745893 DOI: 10.1021/acsptsci.2c00172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Indexed: 11/16/2022]
Abstract
Lung cancer is the leading cause of cancer deaths globally; 1 in 16 people are diagnosed with lung cancer in their lifetime. Microtubules, a critical cytoskeletal assembly, have an essential role in cell division. Interference with the microtubule assembly leads to genetic instability during mitosis and cancer cell death. Currently, available antimitotic drugs such as vincas and taxanes are limited due to side effects such as alopecia, myelosuppression, and drug resistance. Noscapine, an opium alkaloid, is a tubulin-binding agent and can alter the microtubule assembly, causing cancer cell death. Amino acids are fundamental building blocks for protein synthesis, making them essential for the biosynthesis of cancer cells. However, the ability of amino acids in drug transportation has yet to be exploited in developing noscapine analogues as a potential drug candidate for cancer. Hence, in the present study, we have explored the ninth position of noscapine by introducing a hydroxymethylene group using the Blanc reaction and further coupled it with a series of amino acids to construct five target conjugates in good yields. The synthesized amino acid conjugate molecules were biologically evaluated against the A549 lung cancer cell line, among which the noscapine-tryptophan conjugate showed IC50 = 32 μM, as compared to noscapine alone (IC50 = 73 μM). Morphological changes in cancer cells, cell cycle arrest in the G1 phase, and ethidium bromide/acridine orange staining indicated promising anticancer properties. Molecular docking confirmed strong binding to tubulin, with a score of -41.47 kJ/mol with all 3D coordinates and significant involvement of molecular forces, including the hydrogen bonds and hydrophobic interactions. Molecular dynamics simulations demonstrated a stable binding of noscapine-tryptophan conjugate for a prolonged time (100 ns) with the involvement of free energy through the reaction coordinates analyses, solving the bioavailability of parent noscapine to the body.
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Affiliation(s)
- Amardeep Awasthi
- Department of Chemistry, University of Delhi, Delhi-110007, India
| | - Neeraj Kumar
- Department of Neurology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois60611, United States
| | - Abhijeet Mishra
- Department of Biochemistry, Shivaji College, University of Delhi, Delhi-110027, India
| | - Rangnath Ravi
- Department of Chemistry, Shivaji College, University of Delhi, Delhi-110027, India
| | - Anu Dalal
- Department of Chemistry, Indian Institute of Technology, Delhi, Delhi-110016, India
| | - Saurav Shankar
- Department of Chemistry, University of Delhi, Delhi-110007, India
| | - Ramesh Chandra
- Department of Chemistry, University of Delhi, Delhi-110007, India
- Dr. B. R. Ambedkar Centre for Biomedical Research, University of Delhi, Delhi-110007, India
- Institute of Nano Medical Sciences, University of Delhi, Delhi-110007, India
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3
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Chen XF, Zhao X, Yang Z. Aptamer-Based Antibacterial and Antiviral Therapy against Infectious Diseases. J Med Chem 2021; 64:17601-17626. [PMID: 34854680 DOI: 10.1021/acs.jmedchem.1c01567] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nucleic acid aptamers are single-stranded DNA or RNA molecules selected in vitro that can bind to a broad range of targets with high affinity and specificity. As promising alternatives to conventional anti-infective agents, aptamers have gradually revealed their potential in the combat against infectious diseases. This article provides an overview on the state-of-art of aptamer-based antibacterial and antiviral therapeutic strategies. Diverse aptamers targeting pathogen-related components or whole pathogenic cells are summarized according to the species of microorganisms. These aptamers exhibited remarkable in vitro and/or in vivo inhibitory effect for pathogenic invasion, enzymatic activities, or viral replication, even for some highly drug-resistant strains and biofilms. Aptamer-mediated drug delivery and controlled drug release strategies are also included herein. Critical technical barriers of therapeutic aptamers are briefly discussed, followed by some future perspectives for their implementation into clinical utility.
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Affiliation(s)
- Xiao-Fei Chen
- Guangdong Provincial Key Laboratory of Emergency Test for Dangerous Chemicals, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center, Guangzhou), Guangzhou 510070, PR China
| | - Xin Zhao
- Guangdong Provincial Key Laboratory of Emergency Test for Dangerous Chemicals, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center, Guangzhou), Guangzhou 510070, PR China
| | - Zifeng Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, PR China.,Guangzhou Laboratory, Guangzhou 510320, PR China.,Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, Guangzhou 510005, PR China
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Drees A, Fischer M. High-Throughput Selection and Characterisation of Aptamers on Optical Next-Generation Sequencers. Int J Mol Sci 2021; 22:9202. [PMID: 34502110 PMCID: PMC8431662 DOI: 10.3390/ijms22179202] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 02/07/2023] Open
Abstract
Aptamers feature a number of advantages, compared to antibodies. However, their application has been limited so far, mainly because of the complex selection process. 'High-throughput sequencing fluorescent ligand interaction profiling' (HiTS-FLIP) significantly increases the selection efficiency and is consequently a very powerful and versatile technology for the selection of high-performance aptamers. It is the first experiment to allow the direct and quantitative measurement of the affinity and specificity of millions of aptamers simultaneously by harnessing the potential of optical next-generation sequencing platforms to perform fluorescence-based binding assays on the clusters displayed on the flow cells and determining their sequence and position in regular high-throughput sequencing. Many variants of the experiment have been developed that allow automation and in situ conversion of DNA clusters into base-modified DNA, RNA, peptides, and even proteins. In addition, the information from mutational assays, performed with HiTS-FLIP, provides deep insights into the relationship between the sequence, structure, and function of aptamers. This enables a detailed understanding of the sequence-specific rules that determine affinity, and thus, supports the evolution of aptamers. Current variants of the HiTS-FLIP experiment and its application in the field of aptamer selection, characterisation, and optimisation are presented in this review.
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Affiliation(s)
- Alissa Drees
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany;
| | - Markus Fischer
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany;
- Center for Hybrid Nanostructures (CHyN), Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
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Jain A, Prajapati SK, Tripathi M, Raichur AM, Kanwar JR. Exploring the room for repurposed hydroxychloroquine to impede COVID-19: toxicities and multipronged combination approaches with pharmaceutical insights. Expert Rev Clin Pharmacol 2021; 14:715-734. [PMID: 33769888 DOI: 10.1080/17512433.2021.1909473] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Introduction: SARS-CoV-2 has fatally affected the whole world with millions of deaths. Amidst the dilemma of a breakthrough in vaccine development, hydroxychloroquine (HCQ) was looked upon as a prospective repurposed candidate. It has confronted numerous controversies in the past few months as a chemoprophylactic and treatment option for COVID-19. Recently, it has been withdrawn by the World Health Organization for its use in an ongoing pandemic. However, its benefit/risk ratio regarding its use in COVID-19 disease remains poorly justified. An extensive literature search was done using Scopus, PubMed, Google Scholar, www.cdc.gov, www.fda.gov, and who.int.Areas covered: Toxicity vexations of HCQ; pharmaceutical perspectives on new advances in drug delivery approaches; computational modeling (PBPK and PD modeling) overtures; multipronged combination approaches for enhanced synergism with antiviral and anti-inflammatory agents; immuno-boosting effects.Expert commentary: Harnessing the multipronged pharmaceutical perspectives will optimistically help the researchers, scientists, biotech, and pharmaceutical companies to bring new horizons in the safe and efficacious utilization of HCQ alone or in combination with remdesivir and immunomodulatory molecules like bovine lactoferrin in a fight against COVID-19. Combinational therapies with free forms or nanomedicine based targeted approaches can act synergistically to boost host immunity and stop SARS-CoV-2 replication and invasion to impede the infection.
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Affiliation(s)
- Ankit Jain
- Department of Materials Engineering, Indian Institute of Science, Bangalore - Karnataka, India
| | - Shiv Kumar Prajapati
- Department of Pharmaceutical Sciences, Ram-Eesh Institute of Vocational and Technical Education, Greater Noida, Uttar Pradesh, India
| | - Madhavi Tripathi
- Department of Materials Engineering, Indian Institute of Science, Bangalore - Karnataka, India
| | - Ashok M Raichur
- Department of Materials Engineering, Indian Institute of Science, Bangalore - Karnataka, India
| | - Jagat R Kanwar
- Department of Biochemistry, All India Institute of Medical Sciences (AIIMS), Bhopal, Madhya Pradesh, India
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Mugunthan SP, Harish MC. Multi-epitope-Based Vaccine Designed by Targeting Cytoadherence Proteins of Mycoplasma gallisepticum. ACS OMEGA 2021; 6:13742-13755. [PMID: 34095666 PMCID: PMC8173551 DOI: 10.1021/acsomega.1c01032] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/04/2021] [Indexed: 05/18/2023]
Abstract
Mycoplasma gallisepticum causes chronic respiratory disease in chickens leading to large economic losses in the poultry industry, and the impacts remain to be a great challenge for a longer period. Among the other approaches, a vaccine targeting the adhesion proteins of M. gallisepticum would be a promising candidate in controlling the infection. Thus, the present study is aimed to design a multi-epitope vaccine candidate using cytoadhesion proteins of M. gallisepticum through an advanced immunoinformatics approach. As a result, the multi-epitope vaccine was constructed, which comprised potential T-cell and B-cell binding epitopes with appropriate adjuvants. The designed multi-epitope vaccine represented high antigenicity with viable physiochemical properties. The prospective three-dimensional structure of the epitope was predicted, refined, and validated. The molecular docking analysis of multi-epitope vaccine candidates with the chicken Toll-like receptor-5 predicted effective binding. Furthermore, codon optimization and in silico cloning ensured high expression. Thus, the present finding indicates that the engineered multi-epitope vaccine is structurally stable and can induce a strong immune response. Furthermore, the multi-epitope vaccine is suggested to be a suitable vaccine candidate for the M. gallisepticum infection due to its effective binding capacity and precise specificity.
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Affiliation(s)
- Susithra Priyadarshni Mugunthan
- Plant Genetic Engineering and Molecular Farming Lab, Department of Biotechnology, Thiruvalluvar University, Serkkadu, Vellore 632115, Tamil Nadu, India
| | - Mani Chandra Harish
- Plant Genetic Engineering and Molecular Farming Lab, Department of Biotechnology, Thiruvalluvar University, Serkkadu, Vellore 632115, Tamil Nadu, India
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Discovery of ( E)- N-(4-cyanobenzylidene)- 6-fluoro- 3-hydroxypyrazine-2 -carboxamide (cyanorona-20): the first potent and specific anti-COVID-19 drug. CHEMICAL PAPERS 2021; 75:4669-4685. [PMID: 34025012 PMCID: PMC8126404 DOI: 10.1007/s11696-021-01640-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 04/02/2021] [Indexed: 01/18/2023]
Abstract
Abstract Specific inhibition of the viral RNA-dependent RNA polymerase (RdRp) of the newly-emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a very promising strategy for developing highly potent medicines for coronavirus disease 2019 (COVID-19). However, almost all of the reported viral RdRp inhibitors (either repurposed drugs or new antiviral agents) lack selectivity against the SARS-CoV-2 RdRp. Herein, I discovered a new favipiravir derivative, (E)-N-(4-cyanobenzylidene)-6-fluoro-3-hydroxypyrazine-2-carboxamide (cyanorona-20), as the first potent SARS-CoV-2 inhibitor with very high selectivity (209- and 45-fold more potent than favipiravir and remdesivir, respectively). Based on the significant reduction in the in vitro SARS-CoV-2 replication/copies, strong computational cyanorona-20 ligand-RdRp protein interactions, and anti-RdRp activity of the parent favipiravir drug, SARS-CoV-2 inhibition is thought to be mediated through the coronaviral-2 RdRp inhibition. This promising selective anti-COVID-19 compound is also, to the best of our knowledge, the first bioactive derivative of favipiravir, the known antiinfluenza and antiviral drug. This new nucleoside analog was designed, synthesized, characterized, computationally studied (through pharmacokinetic calculations along with computational molecular modeling and prediction), and biologically evaluated for its anti-COVID-19 activities (through a validated in vitro anti-COVID-19 assay). The results of the biological assay showed that cyanorona-20 surprisingly exhibited very significant anti-COVID-19 activity (anti-SARS-CoV-2 EC50 = 0.45 μM), and, in addition, it could be also a very promising lead compound for the design of new anti-COVID-19 agents. Cyanorona-20 is a new favipiravir derivative with promise for the treatment of SARS-CoV-2 infection. Graphic abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1007/s11696-021-01640-9.
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Obaidullah AJ, Alanazi MM, Alsaif NA, Albassam H, Almehizia AA, Alqahtani AM, Mahmud S, Sami SA, Emran TB. Immunoinformatics-guided design of a multi-epitope vaccine based on the structural proteins of severe acute respiratory syndrome coronavirus 2. RSC Adv 2021; 11:18103-18121. [PMID: 35480208 PMCID: PMC9033181 DOI: 10.1039/d1ra02885e] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 05/12/2021] [Indexed: 12/14/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), resulting in a contagious respiratory tract infection that has become a global burden since the end of 2019. Notably, fewer patients infected with SARS-CoV-2 progress from acute disease onset to death compared with the progression rate associated with two other coronaviruses, SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV). Several research organizations and pharmaceutical industries have attempted to develop successful vaccine candidates for the prevention of COVID-19. However, increasing evidence indicates that the SARS-CoV-2 genome undergoes frequent mutation; thus, an adequate analysis of the viral strain remains necessary to construct effective vaccines. The current study attempted to design a multi-epitope vaccine by utilizing an approach based on the SARS-CoV-2 structural proteins. We predicted the antigenic T- and B-lymphocyte responses to four structural proteins after screening all structural proteins according to specific characteristics. The predicted epitopes were combined using suitable adjuvants and linkers, and a secondary structure profile indicated that the vaccine shared similar properties with the native protein. Importantly, the molecular docking analysis and molecular dynamics simulations revealed that the constructed vaccine possessed a high affinity for toll-like receptor 4 (TLR4). In addition, multiple descriptors were obtained from the simulation trajectories, including the root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), solvent-accessible surface area (SASA), and radius of gyration (R g), demonstrating the rigid nature and inflexibility of the vaccine and receptor molecules. In addition, codon optimization, based on Escherichia coli K12, was used to determine the GC content and the codon adaptation index (CAI) value, which further followed for the incorporation into the cloning vector pET28+(a). Collectively, these findings suggested that the constructed vaccine could be used to modulate the immune reaction against SARS-CoV-2.
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Affiliation(s)
- Ahmad J Obaidullah
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University P.O. Box 2457 Riyadh 11451 Saudi Arabia
| | - Mohammed M Alanazi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University P.O. Box 2457 Riyadh 11451 Saudi Arabia
| | - Nawaf A Alsaif
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University P.O. Box 2457 Riyadh 11451 Saudi Arabia
| | - Hussam Albassam
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University P.O. Box 2457 Riyadh 11451 Saudi Arabia
| | - Abdulrahman A Almehizia
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University P.O. Box 2457 Riyadh 11451 Saudi Arabia
| | - Ali M Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University Abha 62529 Saudi Arabia
| | - Shafi Mahmud
- Microbiology Laboratory, Bioinformatics Division, Department of Genetic Engineering and Biotechnology, University of Rajshahi Rajshahi 6205 Bangladesh
| | - Saad Ahmed Sami
- Department of Pharmacy, Faculty of Biological Sciences, University of Chittagong Chittagong 4331 Bangladesh
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh Chittagong 4381 Bangladesh
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In silico approach for Post-SELEX DNA aptamers: A mini-review. J Mol Graph Model 2021; 105:107872. [PMID: 33765525 DOI: 10.1016/j.jmgm.2021.107872] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 02/11/2021] [Accepted: 02/12/2021] [Indexed: 02/07/2023]
Abstract
Aptamers are short oligonucleotides that possess high specificity and affinity against their target. Generated via Systematic Evolution of Ligands by Exponential Enrichment, (SELEX) in vitro, they were screened and enriched. This review covering the study utilizing bioinformatics tools to analyze primary sequence, secondary and tertiary structure prediction, as well as docking simulation for various aptamers and their ligand interaction. Literature was pooled from Web of Science (WoS) and Scopus databases until December 18, 2020 using specific search string related to DNA aptamers, in silico, structure prediction, and docking simulation. Out of 330 published articles, 38 articles were assessed in the analysis based on the predefined inclusion and exclusion criteria. It was found that Mfold and RNA Composer web server is the most popular tool in secondary and tertiary structure prediction of DNA aptamers, respectively. Meanwhile, in docking simulation, ZDOCK and AutoDock are preferred to analyze binding interaction in the aptamer-ligand complex. This review reports a brief framework of recent developments of in silico approaches that provide predictive structural information of ssDNA aptamer.
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Alom MW, Shehab MN, Sujon KM, Akter F. Exploring E, NS3, and NS5 proteins to design a novel multi-epitope vaccine candidate against West Nile Virus: An in-silico approach. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2021.100644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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